Hi all,
I am running a "sample preparation" simulation of an RNA molecule in the water solution with the sodium and chlorine ions, using PMEMD in Amber 9. The timestep necessary for the stability of the heating procedure seems
to strongly depend on the sodium ion concentration that are added in excess
of the sodium concentration that is necessary to neutralize the phosphate
groups in the molecule. To make the simulation run without any exceedances of the velocity limit (vlimit), I have to decrease the timestep
dt approximately 2-fold compared to the simulation of the same system
but without the excess ions. Could you suggest what the source of the
problem could be. Thanks.
Sincerely,
Andrey Semichaevsky
Postdoctoral Research Associate,
Materials Science and Engineering,
North Carolina State University,
Raleigh NC
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Received on Sun Jan 20 2008 - 06:07:17 PST
